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Kwok, Kirsty TT; de Rooij, Myrna MT; Messink, Aniek B; Wouters, Inge M; Smit, Lidwien AM; Cotten, Matthew; Heederik, Dick JJ; Koopmans, Marion PG; Phan, My VT; (2022) Establishing farm dust as a useful viral metagenomic surveillance matrix. Sci Rep, 12 (1). 16308-. DOI: https://doi.org/10.1038/s41598-022-20701-x

Molendijk, Michèle M; Phan, My VT; Bode, Lonneke GM; Strepis, Nikolas; Prasad, Divyae K; Worp, Nathalie; Nieuwenhuijse, David F; Schapendonk, Claudia ME; Boekema, Bouke KHL; Verbon, Annelies; +3 more... Koopmans, Marion PG; Graaf, Miranda de; van Wamel, Willem JB; (2022) Microcalorimetry: A Novel Application to Measure In Vitro Phage Susceptibility of Staphylococcus aureus in Human Serum. Viruses, 15 (1). p. 14. ISSN 1999-4915 DOI: https://doi.org/10.3390/v15010014

Namuwulya, Prossy; Bukenya, Henry; Tushabe, Phionah; Tweyongyere, Robert; Bwogi, Josephine; Cotten, Matthew; Phan, My VT; (2022) Near-Complete Genome Sequences of Measles Virus Strains from 10 Years of Uganda Country-wide Surveillance. Microbiology Resource Announcements, 11 (8). e0060622-. ISSN 2576-098X DOI: https://doi.org/10.1128/mra.00606-22

Phan, My VT; Agoti, Charles N; Munywoki, Patrick K; Otieno, Grieven P; Ngama, Mwanajuma; Kellam, Paul; Cotten, Matthew; Nokes, D James; (2022) Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya. Scientific reports, 12 (1). 202-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-021-03987-1

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Allesøe, Rosa L; Lemvigh, Camilla K; Phan, My VT; Clausen, Philip TLC; Florensa, Alfred F; Koopmans, Marion PG; Lund, Ole; Cotten, Matthew; (2021) Automated download and clean-up of family-specific databases for kmer-based virus identification. Bioinformatics (Oxford, England), 37 (5). pp. 705-710. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/btaa857

Bugembe, Daniel Lule; Phan, My VT; Abias, Abe G; Ayei, James; Deng, Lul Lojok; Lako, Richard Lino Loro; Rumunu, John; Kaleebu, Pontiano; Wamala, Joseph Francis; Hm, Juma John; +3 more... Lodiongo, Dennis Kenyi; Bunga, Sudhir; Cotten, Matthew; (2021) SARS-CoV-2 Variants, South Sudan, January-March 2021. Emerging Infectious Diseases, 27 (12). pp. 3133-3136. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2712.211488

Bugembe, Daniel Lule; Phan, My VT; Ssewanyana, Isaac; Semanda, Patrick; Nansumba, Hellen; Dhaala, Beatrice; Nabadda, Susan; O'Toole, Áine Niamh; Rambaut, Andrew; Kaleebu, Pontiano; +1 more... Cotten, Matthew; (2021) Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda. Nature microbiology, 6 (8). pp. 1094-1101. ISSN 2058-5276 DOI: https://doi.org/10.1038/s41564-021-00933-9

Cotten, Matthew; Robertson, David L; Phan, My VT; (2021) Unique protein features of SARS-CoV-2 relative to other Sarbecoviruses. Virus evolution, 7 (2). veab067-. ISSN 2057-1577 DOI: https://doi.org/10.1093/ve/veab067

Kwok, Kirsty TT; de Rooij, Myrna MT; Sinartio, Felisita F; Smit, Lidwien AM; Koopmans, Marion PG; Phan, My VT; (2021) Genome Sequence of a Minacovirus Strain from a Farmed Mink in The Netherlands. Microbiology resource announcements, 10 (8). ISSN 2576-098X DOI: https://doi.org/10.1128/MRA.01451-20

Lambisia, Arnold W; Phan, My VT; de Laurent, Zaydah R; Cotten, Matthew; Nokes, D James; Agoti, Charles N; (2021) Near-Complete Genome Sequences of Eight Human Astroviruses Recovered from Diarrheal Stool Samples of Hospitalized Children in Coastal Kenya in 2019. Microbiology resource announcements, 10 (15). e00162-e00121. ISSN 2576-098X DOI: https://doi.org/10.1128/MRA.00162-21

Roach, Michael; Cantu, Adrian; Vieri, Melissa Krizia; Cotten, Matthew; Kellam, Paul; Phan, My; Hoek, Lia van der; Mandro, Michel; Tepage, Floribert; Mambandu, Germain; +5 more... Musinya, Gisele; Laudisoit, Anne; Colebunders, Robert; Edwards, Robert; Mokili, John L; (2021) No Evidence Known Viruses Play a Role in the Pathogenesis of Onchocerciasis-Associated Epilepsy. An Explorative Metagenomic Case-Control Study. Pathogens (Basel, Switzerland), 10 (7). p. 787. ISSN 2076-0817 DOI: https://doi.org/10.3390/pathogens10070787

Wilkinson, Eduan; Giovanetti, Marta; Tegally, Houriiyah; San, James E; Lessells, Richard; Cuadros, Diego; Martin, Darren P; Rasmussen, David A; Zekri, Abdel-Rahman N; Sangare, Abdoul K; +292 more... 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Wiley, Michael R; Youtchou, Mirabeau T; Ayekaba, Mitoha O; Abouelhoda, Mohamed; Seadawy, Mohamed G; Khalifa, Mohamed K; Sekhele, Mooko; Ouadghiri, Mouna; Diagne, Moussa M; Mwenda, Mulenga; Allam, Mushal; Phan, My VT; Abid, Nabil; Touil, Nadia; Rujeni, Nadine; Kharrat, Najla; Ismael, Nalia; Dia, Ndongo; Mabunda, Nedio; Hsiao, Nei-Yuan; Silochi, Nelson B; Nsenga, Ngoy; Gumede, Nicksy; Mulder, Nicola; Ndodo, Nnaemeka; Razanajatovo, Norosoa H; Iguosadolo, Nosamiefan; Judith, Oguzie; Kingsley, Ojide C; Sylvanus, Okogbenin; Peter, Okokhere; Femi, Oladiji; Idowu, Olawoye; Testimony, Olumade; Chukwuma, Omoruyi E; Ogah, Onwe E; Onwuamah, Chika K; Cyril, Oshomah; Faye, Ousmane; Tomori, Oyewale; Ondoa, Pascale; Combe, Patrice; Semanda, Patrick; Oluniyi, Paul E; Arnaldo, Paulo; Quashie, Peter K; Dussart, Philippe; Bester, Phillip A; Mbala, Placide K; Ayivor-Djanie, Reuben; Njouom, Richard; Phillips, Richard O; Gorman, Richmond; Kingsley, Robert A; Carr, Rosina AA; El Kabbaj, Saâd; Gargouri, Saba; 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Bugembe, Daniel Lule; Kayiwa, John; Phan, My VT; Tushabe, Phiona; Balinandi, Stephen; Dhaala, Beatrice; Lexow, Jonas; Mwebesa, Henry; Aceng, Jane; Kyobe, Henry; +4 more... Ssemwanga, Deogratius; Lutwama, Julius; Kaleebu, Pontiano; Cotten, Matthew; (2020) Main Routes of Entry and Genomic Diversity of SARS-CoV-2, Uganda. EMERGING INFECTIOUS DISEASES, 26 (10). pp. 2411-2415. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2610.202575

Kamau, Everlyn; Oketch, John W; de Laurent, Zaydah R; Phan, My VT; Agoti, Charles N; Nokes, D James; Cotten, Matthew; (2020) Correction to: Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia. BMC genomics, 21 (1). 83-. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-020-6498-z

Kamau, Everlyn; Oketch, John W; de Laurent, Zaydah R; Phan, My VT; Agoti, Charles N; Nokes, D James; Cotten, Matthew; (2020) Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia. BMC GENOMICS, 21 (1). 5-. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-019-6400-z

Kwok, Kirsty TT; Nieuwenhuijse, David F; Phan, My VT; Koopmans, Marion PG; (2020) Virus Metagenomics in Farm Animals: A Systematic Review. VIRUSES-BASEL, 12 (1). p. 107. ISSN 1999-4915 DOI: https://doi.org/10.3390/v12010107

Masembe, Charles; Phan, My VT; Robertson, David L; Cotten, Matthew; (2020) Increased resolution of African swine fever virus genome patterns based on profile HMMs of protein domains. Virus evolution, 6 (2). veaa044-. ISSN 2057-1577 DOI: https://doi.org/10.1093/ve/veaa044

Nieuwenhuijse, David F; Oude Munnink, Bas B; Phan, My VT; Global Sewage Surveillance project consortium; Munk, Patrick; Venkatakrishnan, Shweta; Aarestrup, Frank M; Cotten, Matthew; Koopmans, Marion PG; (2020) Setting a baseline for global urban virome surveillance in sewage. Scientific reports, 10 (1). 13748-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-020-69869-0

Phan, My VT; Mendonca Melo, Mariana; van Nood, Els; Aron, Georgina; Kreeft-Voermans, Jolanda JC; Koopmans, Marion PG; Reusken, Chantal; GeurtsvanKessel, Corine H; Cotten, Matthew; (2020) Shedding of Yellow Fever Virus From an Imported Case in the Netherlands After Travel to Brazil. OPEN FORUM INFECTIOUS DISEASES, 7 (2). ofaa020-. ISSN 2328-8957 DOI: https://doi.org/10.1093/ofid/ofaa020

Sips, Gregorius J; Dirven, Mariëlle JG; Donkervoort, Joke T; van Kolfschoten, Francien M; Schapendonk, Claudia ME; Phan, My VT; Bloem, Annemieke; van Leeuwen, Anna F; Trompenaars, Mariechristine E; Koopmans, Marion PG; +3 more... van der Eijk, Annemiek A; de Graaf, Miranda; Fanoy, Ewout B; (2020) Norovirus outbreak in a natural playground: A One Health approach. Zoonoses and Public Health, 67 (4). pp. 453-459. ISSN 1863-1959 DOI: https://doi.org/10.1111/zph.12689

Agoti, Charles N; Phan, My VT; Munywoki, Patrick K; Githinji, George; Medley, Graham F; Cane, Patricia A; Kellam, Paul; Cotten, Matthew; Nokes, D James; (2019) Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant. Scientific reports, 9 (1). 10076-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-019-46509-w

Kamau, Everlyn; Agoti, Charles N; Ngoi, Joyce M; de Laurent, Zaydah R; Gitonga, John; Cotten, Matthew; Phan, My VT; Nokes, D James; Delwart, Eric; Sanders, Eduard; +1 more... Warimwe, George M; (2019) Complete Genome Sequences of Dengue Virus Type 2 Strains from Kilifi, Kenya. Microbiology Resource Announcements, 8 (4). ISSN 2576-098X DOI: https://doi.org/10.1128/MRA.01566-18

Phan, My VT; Arron, Georgina; GeurtsvanKessel, Corine H; Huisman, Robin C; Molenkamp, Richard; Koopmans, Marion PG; Cotten, Matthew; (2019) Complete Genome Characterization of Eight Human Parainfluenza Viruses from the Netherlands. MICROBIOLOGY RESOURCE ANNOUNCEMENTS, 8 (15). ISSN 2576-098X DOI: https://doi.org/10.1128/MRA.00125-19

Phan, My Vt; Murad, Sarwa Darwish; van der Eijk, Annemiek A; Metselaar, Herold J; Hartog, Hermien; Harinck, Femme; GeurtsvanKessel, Corine H; Molenkamp, Richard; Cotten, Matthew; Koopmans, Marion Pg; (2019) Genomic sequence of yellow fever virus from a Dutch traveller returning from the Gambia-Senegal region, the Netherlands, November 2018. Eurosurveillance: Europe's journal on infectious disease surveillance, epidemiology, prevention and control, 24 (4). pp. 15-18. ISSN 1025-496X DOI: https://doi.org/10.2807/1560-7917.ES.2019.24.4.1800684

Strubbia, Sofia; Phan, My VT; Schaeffer, Julien; Koopmans, Marion; Cotten, Matthew; Le Guyader, Françoise S; (2019) Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing. FOOD AND ENVIRONMENTAL VIROLOGY, 11 (4). pp. 400-409. ISSN 1867-0334 DOI: https://doi.org/10.1007/s12560-019-09402-3

Strubbia, Sofia; Schaeffer, Julien; Oude Munnink, Bas B; Besnard, Alban; Phan, My VT; Nieuwenhuijse, David F; de Graaf, Miranda; Schapendonk, Claudia ME; Wacrenier, Candice; Cotten, Matthew; +2 more... Koopmans, Marion PG; Le Guyader, Françoise S; (2019) Metavirome Sequencing to Evaluate Norovirus Diversity in Sewage and Related Bioaccumulated Oysters. Frontiers in Microbiology, 10 (OCT). 2394-. ISSN 1664-302X DOI: https://doi.org/10.3389/fmicb.2019.02394

Tapinos, Avraam; Constantinides, Bede; Phan, My VT; Kouchaki, Samaneh; Cotten, Matthew; Robertson, David L; (2019) The Utility of Data Transformation for Alignment, De Novo Assembly and Classification of Short Read Virus Sequences. VIRUSES-BASEL, 11 (5). p. 394. ISSN 1999-4915 DOI: https://doi.org/10.3390/v11050394

Phan, My VT; Ngo Tri, Tue; Hong Anh, Pham; Baker, Stephen; Kellam, Paul; Cotten, Matthew; (2018) Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains. VIRUS EVOLUTION, 4 (2). vey035-. ISSN 2057-1577 DOI: https://doi.org/10.1093/ve/vey035

Phan, My VT; Schapendonk, Claudia ME; Oude Munnink, Bas B; Koopmans, Marion PG; de Swart, Rik L; Cotten, Matthew; (2018) Complete Genome Sequences of Six Measles Virus Strains. Microbiology Resource Announcements, 6 (13). e00184-18. ISSN 2576-098X DOI: https://doi.org/10.1128/genomeA.00184-18

Agoti, Charles N; Munywoki, Patrick K; Phan, My VT; Otieno, James R; Kamau, Everlyn; Bett, Anne; Kombe, Ivy; Githinji, George; Medley, Graham F; Cane, Patricia A; +3 more... Kellam, Paul; Cotten, Matthew; Nokes, D James; (2017) Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis. Virus evolution, 3 (1). vex006-. ISSN 2057-1577 DOI: https://doi.org/10.1093/ve/vex006

Fraaij, Pieter LA; Wildschut, Enno D; Houmes, Robert J; Swaan, Corien M; Hoebe, Christian J; de Jonge, HCC; Tolsma, Paulien; de Kleer, Isme; Pas, Suzan D; Oude Munnink, Bas B; +10 more... Phan, My VT; Bestebroer, Theo M; Roosenhoff, R Shanty; van Kampen, Jeroen JA; Cotten, Matthew; Beerens, Nancy; Fouchier, Ron AM; van den Kerkhof, Johannes H; Timen, Aura; Koopmans, Marion P; (2016) Severe acute respiratory infection caused by swine influenza virus in a child necessitating extracorporeal membrane oxygenation (ECMO), the Netherlands, October 2016. EUROSURVEILLANCE, 21 (48). pp. 8-10. ISSN 1560-7917 DOI: https://doi.org/10.2807/1560-7917.ES.2016.21.48.30416

Oude Munnink, Bas B; Phan, My VT; van der Hoek, Lia; Kellam, Paul; Cotten, Matthew; VIZIONS Consortium; (2016) Genome Sequences of a Novel Vietnamese Bat Bunyavirus. Microbiology Resource Announcements, 4 (6). e01366-16. ISSN 2576-098X DOI: https://doi.org/10.1128/genomeA.01366-16

Phan, My VT; Anh, Pham Hong; Cuong, Nguyen Van; Munnink, Bas B Oude; van der Hoek, Lia; My, Phuc Tran; Tri, Tue Ngo; Bryant, Juliet E; Baker, Stephen; Thwaites, Guy; +5 more... Woolhouse, Mark; Kellam, Paul; Rabaa, Maia A; Cotten, Matthew; VIZIONS Consortium; (2016) Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection. Virus evolution, 2 (2). vew027-. ISSN 2057-1577 DOI: https://doi.org/10.1093/ve/vew027

Thompson, Corinne N; Phan, My VT; Hoang, Nguyen Van Minh; Minh, Pham Van; Vinh, Nguyen Thanh; Thuy, Cao Thu; Nga, Tran Thi Thu; Rabaa, Maia A; Duy, Pham Thanh; Dung, Tran Thi Ngoc; +19 more... Phat, Voong Vinh; Nga, Tran Vu Thieu; Tu, Le Thi Phuong; Tuyen, Ha Thanh; Yoshihara, Keisuke; Jenkins, Claire; Duong, Vu Thuy; Phuc, Hoang Le; Tuyet, Pham Thi Ngoc; Ngoc, Nguyen Minh; Vinh, Ha; Chinh, Nguyen Tran; Thuong, Tang Chi; Tuan, Ha Manh; Hien, Tran Tinh; Campbell, James I; Chau, Nguyen Van Vinh; Thwaites, Guy; Baker, Stephen; (2015) A prospective multi-center observational study of children hospitalized with diarrhea in Ho Chi Minh City, Vietnam. The American journal of tropical medicine and hygiene, 92 (5). pp. 1045-1052. ISSN 0002-9637 DOI: https://doi.org/10.4269/ajtmh.14-0655

Thompson, Corinne N; Zelner, Jonathan L; Nhu, Tran Do Hoang; Phan, My Vt; Hoang Le, Phuc; Nguyen Thanh, Hung; Vu Thuy, Duong; Minh Nguyen, Ngoc; Ha Manh, Tuan; Van Hoang Minh, Tu; +8 more... Lu Lan, Vi; Nguyen Van Vinh, Chau; Tran Tinh, Hien; von Clemm, Emmiliese; Storch, Harry; Thwaites, Guy; Grenfell, Bryan T; Baker, Stephen; (2015) The impact of environmental and climatic variation on the spatiotemporal trends of hospitalized pediatric diarrhea in Ho Chi Minh City, Vietnam. Health & place, 35. pp. 147-154. ISSN 1353-8292 DOI: https://doi.org/10.1016/j.healthplace.2015.08.001

Cotten, Matthew; Petrova, Velislava; Phan, My VT; Rabaa, Maia A; Watson, Simon J; Ong, Swee Hoe; Kellam, Paul; Baker, Stephen; (2014) Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting. Journal of virology, 88 (19). pp. 11056-11069. ISSN 0022-538X DOI: https://doi.org/10.1128/JVI.01333-14